DHS nominee under investigation for allegedly helping Hillary Clinton's brother

May 11, 2010: Immigration Services Director (USCIS) Alejandro Mayorkas listens to a question on Capitol Hill in Washington. (AP)

Authorities are investigating the man President Obama tapped to take over the second highest spot at the Department of Homeland Security for allegedly using his position and power to unfairly obtain U.S. visas for foreign investors in a company run by Hillary Clinton’s brother, FoxNews.com has confirmed.

Alejandro Mayorkas, director of the U.S. Citizenship and Immigration Services, was named by Homeland Security's Inspector General's Office as a target in an investigation involving the foreign investor program run by USCIS, according to an email sent to lawmakers late Monday.

The investigation was opened in September 2012 following a referral from an FBI counterintelligence analyst. The probe was first reported by The Associated Press.

The investigation into Mayorkas is based on allegations he helped secure U.S. visas for Chinese businessmen after they had been denied by his own agency’s officials. The visas had been sought by Gulf Coast Funds Management, a financing company headed by then-Secretary of State Clinton’s brother Anthony Rodham, according to an aide to GOP Sen. Charles Grassley, who had received internal USCIS emails about the matter from a department whistle-blower.

According to an email sent to lawmakers Monday, the IG's office said, "At this point in our investigation, we do not have any findings of criminal misconduct." The email did not specify any criminal allegations it might be investigating.

White House press secretary Jay Carney referred questions to the inspector general's office, which said that the probe is in its preliminary stage and that it doesn't comment on the specifics of investigations.

The program, known as EB-5, allows foreigners to get visas if they invest $500,000 to $1 million in projects or businesses that create jobs for U.S. citizens. The amount of the investment required depends on the type of project. Investors who are approved for the program can become legal permanent residents after two years and can later be eligible to become citizens.

If Mayorkas were confirmed as Homeland Security's deputy secretary, he probably would run the department until a permanent replacement was approved to take over for departing Secretary Janet Napolitano.

The email to lawmakers said the primary complaint against Mayorkas was that he helped a financing company run by Rodham  to win approval for an investor visa, even after the application was denied and an appeal was rejected.

Mayorkas, a former U.S. attorney in California, previously came under criticism for his involvement in the commutation by President Bill Clinton of the prison sentence of the son of a Democratic Party donor.

Another of Hillary Clinton's brothers, Hugh Rodham, had been hired by the donor to lobby for the commutation. Mayorkas told lawmakers during his 2009 confirmation hearing that "it was a mistake" to talk to the White House about the request.

Hillary Clinton, who stepped down as secretary of state on Feb. 1, is considered a possible contender for the Democratic presidential nomination in 2016.

According to the Inspector General's email, the investigation of the investor visa program also includes allegations that other USCIS Office of General Counsel officials obstructed an audit of the visa program by the Securities and Exchange Commission. The email did not name any specific official from the general counsel's office.

The email says investigators did not know whether Mayorkas was aware of the investigation.

The FBI's Washington field office was told about the investigation in June after it inquired about Mayorkas as part of the White House background investigation for his nomination as deputy DHS secretary.

The FBI in Washington has been concerned about the investor visa program and the projects funded by foreign sources since at least March, according to emails obtained by The AP.

The bureau wanted details of all of the limited liability companies that had invested in the EB-5 visa program. Of particular concern, the FBI official wrote, was Chinese investment in projects, including the building of an FBI facility.

"Let's just say that we have a significant issue that my higher-ups are really concerned about and this may be addressed way above my pay grade," an official wrote in one email. The FBI official's name was redacted in that email.

Iowa Sen. Charles Grassley, the ranking Republican on the Senate Judiciary Committee, sent the FBI a lengthy letter Tuesday asking for details of its review of the foreign investor visa program and Chinese investment in U.S. infrastructure projects.

Chinese investment in infrastructure projects has long been a concern of the U.S. government. In September, the Obama administration blocked a Chinese company from owning four wind farm projects in northern Oregon that were near a Navy base used to fly unmanned drones and electronic-warfare planes on training missions. In October, the House Intelligence Committee warned that two leading Chinese technology firms, Huawei Technologies Ltd. and ZTE Corp., posed a major security threat to the U.S. Both firms have denied being influenced by the Chinese government.

The most routine users of the EB-5 program are Chinese investors.

According to an undated, unclassified State Department report about the program obtained by the AP, the U.S. Consulate in Guangzhou, China, processed more investor visas in the 2011 fiscal year than any other consulate or embassy.

The document says "applicants are usually coached and prepped for their interviews, making it difficult to take at face value applicants' claims" about where their money comes from and whether they hold membership in the Chinese Communist Party. Party membership would make an applicant ineligible for the investor visa.

Anthony Rodham is president and CEO of Gulf Coast Funds Management LLC in McLean, Va. The firm is one of hundreds of "Regional Centers" that pool investments from foreign nationals looking to invest in U.S. businesses or industries as part of the foreign investor visa program.

There was no immediate response to an email sent to Gulf Coast requesting comment.

It is unclear from the IG's email why the investor visa application was denied. Visa requests can be denied for a number of reasons, including a circumstance where an applicant has a criminal background or is considered a threat to national security or public safety.

Fox News' Jana Winter and The Associated Press contributed to this report.